title: Computational analysis of looping of a large family of highly bent DNA by LacI.
abstract: Sequence-dependent intrinsic curvature of DNA influences looping by regulatory proteins such as LacI and NtrC. Curvature can enhance stability and control shape, as observed in LacI loops formed with three designed sequences with operators bracketing an A-tract bend. We explore geometric, topological, and energetic effects of curvature with an analysis of a family of highly bent sequences, using the elastic rod model from previous work. A unifying straight-helical-straight representation uses two phasing parameters to describe sequences composed of two straight segments that flank a common helically supercoiled segment. We exercise the rod model over this two-dimensional space of phasing parameters to evaluate looping behaviors. This design space is found to comprise two subspaces that prefer parallel versus anti-parallel binding topologies. The energetic cost of looping varies from 4 to 12 kT. Molecules can be designed to yield distinct binding topologies as well as hyperstable or hypostable loops and potentially loops that can switch conformations. Loop switching could be a mechanism for control of gene expression. Model predictions for linking numbers and sizes of LacI-DNA loops can be tested using multiple experimental approaches, which coupled with theory could address whether proteins or DNA provide the observed flexibility of protein-DNA loops.
authors.affiliation: Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Todd D
authors.initials: TD
authors.lastname: Lillian
authors.forename: Sachin
authors.initials: S
authors.lastname: Goyal
authors.forename: Jason D
authors.initials: JD
authors.lastname: Kahn
authors.forename: Edgar
authors.initials: E
authors.lastname: Meyhöfer
authors.forename: N C
authors.initials: NC
authors.lastname: Perkins
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism* / Q000494:pharmacology; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004548:Elasticity; D056968:Lac Repressors; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012097:Repressor Proteins / Q000378:metabolism* / Q000494:pharmacology; D015203:Reproducibility of Results; D012399:Rotation; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D056968:Lac Repressors; D012097:Repressor Proteins; D004247:DNA